Python API for paircomp

The Python API for paircomp is a simple object-oriented interface.
There are only two classes, the Comparison class and the Match class.
Only the Comparison class has any methods; the Match class is strictly
a container for a pairwise match.

The file tests/test-python-interface.py contains all of these commands
in their native glory, if you'd like to see them actually running.

Note: All of the time-consuming functions respect threading, so you
can run the functions in parallel on multiprocessor machines.

One additional function of note is filter_transitively, which
filters paths between sequences A, B, and C such that only paths
connecting the same points from A to B, B to C, and A to C remain.

The function call is

new_ab, new_bc, new_ac = paircomp.filter_transitively(ab, bc, ac)

and it takes three pairwise comparisons, A-->B, B-->C, and A-->C,
all done with the same windowsize (threshold may vary). The
function returns three new comparisons, filtered transitively. For
a graphical demonstration of this feature, see the FamilyRelationsII
program.

Note: this function may be very slow for sequences containing many
repeats.

Another function, build_transitive, builds the new_ac comparison
(above) from A-->B and B-->C comparisons. It's primarily there to test
filter_transitively, but if you want to use it you can call it like
so: